At 71, he was elected patriarch of the Maronites on 15 March 2011,[5] after getting more than two-thirds of the votes of the 39 bishops and replacing Nasrallah Sfeir.[6] The new patriarch formally requested and received ecclesiastical communion from Pope Benedict XVI on 24 March 2011 pursuant to Canon 76 § 2 of the Code of Canons of the Eastern Churches.[7][8] The Mass for the inauguration of his Patriarchate took place on 25 March 2011, in Bkerké, the see of the Maronite Catholic Patriarchate. As is customary for all Maronite Patriarchs, Patriarch al-Rahi took the additional name Boutros, that of Saint Peter, who briefly held the See of Antioch before moving to Rome to become Bishop there. On 7 March 2012, Patriarch al-Rahi was appointed a member of the Congregation for the Oriental Churches.[9]

On 18 March 2015 al-Rahi became the sole cardinal-elector from the order of cardinal-bishops when Cardinal Naguib turned 80. He remained the sole cardinal-bishop elector until 28 June 2018 when four Latin church cardinal-priests of voting age were elevated by Pope Francis to cardinal-bishop by having their titular churches co-opted to suburbicarian rank.[16][17] and Louis Raphaël I Sako, Patriarch of the Chaldean Catholic Church was created a cardinal-patriarch.[18]

In April 2011, al-Rahi said that, for the sake of communion and love, he would work "to establish a sincere and complete dialogue" with Muslims "and build together a future in common life and cooperation." He said his predecessor "struggled with insistence to free both the national decision-making and the land of Lebanon from all forms of tutelage and occupation, worked for reconciliation in Mount Lebanon and realized needed church reforms. All of these constitute an extension of the church's springtime started by the Second Vatican Council."[19] Patriarch al-Rahi does not use the term "Arab Spring", but "Arab Winter" to express his unenthusiastic reaction.[20]

In September 2011, some of the Christian supporters of the March 14 alliance were upset over his controversial comments in Paris, France where he supported Hezbollah's right to hold arms in defense against Israel, and stated that the 2011 Syrian protests could awaken the rise of the Muslim Brotherhood if President Bashar al-Assad was removed from office. 14 March supporters stressed how his predecessor had very different views and was almost fanatically supportive of the Lebanese Forces. Christian supporters of the March 8 alliance welcomed his comments. Prime Minister Najib Mikati also supported his stance saying "The Maronite patriarch spoke about a part [of the problem]. No one is against the resistance’s arms as long as Israeli occupation continues. There is Lebanese unanimity on the resistance’s arms in the face of Israeli occupation." [21] Mikati said after his meeting with al-Rahi that he was "very relieved and reassured by the Patriarch’s wisdom."[22] President Michel Suleiman said that "the Patriarch is not in need of anyone to defend him and his positions emanate from his central role as a person in charge of Lebanon's and the Middle East's Christians and that of Lebanon's independence and sovereignty;"[23] and that "the patriarch does not need to be defended, and his stances represent his way of taking responsibility for Lebanon's Christians."[24]

Parliament speaker Nabih Berri said that al-Rahi's "comments in Paris protect Lebanon from danger and I agree with what he stated and affirm his vision that is rooted in both a religious and national background" and that "If the situation further deteriorated in Syria and we reached a more radical rule than the current rule, like the rule of the Muslim Brotherhood, Christians there would pay the price, either in the form of killings or displacement. Here is the picture of Iraq in front of us."[25]

Free Patriotic Movement leader Michel Aoun expressed support for al-Rahi: "Rai’s statements express the concerns of the minorities because he is entrusted with the Synod for the Middle East. Gradual changes doesn’t harm stability and wouldn’t get Syria into the [same] troubles as Palestine, Iraq, Libya and Yemen. [As some of the Syrian demonstrators are armed and are destroying the country] the Syrian government cannot but bring order to the country."[26] Former 14 March Progressive Socialist Party leader Walid Jumblatt also criticised al-Rahi's assessment on the grounds that "Lebanon cannot remain hostage to regional conflicts", and denied that regime change in Syria was posing a threat to Christians in the country.[27]

In an interview with Reuters on 4 March 2012, al-Rahi said: "All regimes in the Arab world have Islam as a state religion, except for Syria. It stands out for not saying it is an Islamic state...The closest thing to democracy [in the Arab world] is Syria."[28]

On 26 May 2014, the patriarch decided to join Pope Francis on parts of the pontifical three-day Holy Land pilgrimage. The Maronite patriarch arrived late Sunday in Jerusalem after accompanying Francis in the West Bank, but he departed from the parts of the Catholic leader's itinerary that involved meetings with Israeli officials. After visiting a monastery outside the city on his way to Jaffa, al-Rahi joined the Pope again in the afternoon for Mass at Jerusalem's Cenacle. The patriarch then returned to the West Bank for a visit to Beit Sahour, toured the north, the Galilee region, Nazareth, Acre and Haifa, where many of the country's Arab Christian minority live.
The visit was criticized at home. The patriarch maintained that he was misunderstood and that his journey was celebrating the roots of Christianity in the region.[29]

^The first two Maronite Cardinals Paul Peter Meouchi (made cardinal by Pope Paul VI) and Anthony Peter Khoraish (created cardinal by Pope John Paul II) turned 80 and died before having an opportunity to participate in a conclave and the third Maronite Patriarch to become a cardinal, Nasrallah Boutros Sfeir was over the age of 80 during the 2005 sede vacante and thus did not take part in that year's conclave.